BioC 2.14: CHECK report for SLGI on petty

Package: SLGI

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SLGI_1.24.0.tar.gz

StartedAt: 2014-10-08 00:09:35 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:19:20 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 584.5 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SLGI_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/SLGI.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.24.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SLGI’ can be installed ... [23s/25s] OK
* checking installed package size ... NOTE
  installed size is 15.9Mb
  sub-directories of 1Mb or more:
    data      4.2Mb
    extdata  11.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ScISI’ ‘lattice’ ‘GO.db’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [291s/302s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        55.365  3.237  61.319
plot            29.439  8.429  38.239
compare         29.775  5.979  36.545
siResult-class  27.333  7.937  36.799
modelSLGI       25.884  8.494  35.371
topInteraction  14.321  3.753  18.476
twoWayTable     15.950  0.285  16.447
normInteraction 11.930  4.203  16.880
AtongFnDomain    8.795  0.268   9.196
sharedBy         5.054  0.147   5.221
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/SLGI.Rcheck/00check.log’
for details.

* installing *source* package ‘SLGI’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "BiocGenerics" for requests: plot
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: plot
* DONE (SLGI)

name	user	system	elapsed
Atong	0.015	0.006	0.043
AtongFnDomain	8.795	0.268	9.196
AtongPair	0.648	0.067	0.752
SDL	0.013	0.002	0.048
SGA	0.012	0.045	0.106
SGD.SL	0.224	0.050	0.398
TFmat	0.106	0.054	0.216
byComplex	0.598	0.137	0.929
comemberIn	1.206	0.180	1.437
compare	29.775	5.979	36.545
congruence	0.005	0.001	0.007
createSquareMatrix	0.603	0.067	0.690
domainDist	4.580	0.162	4.854
essglist	0.021	0.008	0.094
getInteraction	0.007	0.001	0.008
getSharedDomains	0.465	0.024	0.788
getSharedInteraction	0.005	0.000	0.009
getTestedPairs	0.024	0.001	0.026
getUniquePairs	0.330	0.002	0.341
gi2005	0.081	0.049	0.160
gi2007	0.685	0.070	0.836
gi2Interactome	0.002	0.000	0.003
hyperG	0.011	0.001	0.012
iSummary	55.365	3.237	61.319
modelSLGI	25.884	8.494	35.371
normInteraction	11.930	4.203	16.880
plot	29.439	8.429	38.239
seqMatcherAlign	0.002	0.001	0.002
sharedBy	5.054	0.147	5.221
sharedInt	0.008	0.000	0.008
siResult-class	27.333	7.937	36.799
test2Interact	0.008	0.000	0.008
topInteraction	14.321	3.753	18.476
twoWayTable	15.950	0.285	16.447
withinComplex	1.895	0.214	2.143